Title :
Towards Fast Bioinformatics Algorithms: Benchmarking the GPGPU
Author :
Alic, Andrei ; Visan, Simona ; Potolea, Rodica
Author_Institution :
Tech. Univ. of Cluj-Napoca, Cluj-Napoca, Romania
Abstract :
This paper studies the viability of GPGPU, by analyzing the speedup of 9 algorithms frequently used in practice. The speedup we have obtained suggests the possibility of implementing fast versions of Levenshtein distance and Knuth-Morris-Pratt exact search, required by many bioinformatics applications.
Keywords :
bioinformatics; computer graphic equipment; coprocessors; GPGPU; Knuth-Morris-Pratt exact search; Levenshtein distance; fast bioinformatics algorithm; general purpose graphics processing unit; Arrays; Bioinformatics; Clustering algorithms; Graphics processing unit; Instruction sets; Partitioning algorithms; Random access memory; GPGPU; bioinformatics; implementation; parallel algorithms;
Conference_Titel :
Parallel and Distributed Computing (ISPDC), 2011 10th International Symposium on
Conference_Location :
Cluj Napoca
Print_ISBN :
978-1-4577-1536-5
DOI :
10.1109/ISPDC.2011.45
